diff --git a/configure b/configure
index c935bad4b88e8c1b54ffc657c001f9f52a23033a..ba94dc2b4ec2da43b77e94e9fe8036692a4e4aab 100755
--- a/configure
+++ b/configure
@@ -1,8 +1,8 @@
#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for sybilSBML 2.0.8.
+# Generated by GNU Autoconf 2.69 for sybilSBML 3.0.0.
#
-# Report bugs to <geliudie@uni-duesseldorf.de>.
+# Report bugs to <clausjonathan.fritzemeier@uni-duesseldorf.de>.
#
#
# Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc.
@@ -267,8 +267,8 @@ fi
$as_echo "$0: be upgraded to zsh 4.3.4 or later."
else
$as_echo "$0: Please tell bug-autoconf@gnu.org and
-$0: geliudie@uni-duesseldorf.de about your system,
-$0: including any error possibly output before this
+$0: clausjonathan.fritzemeier@uni-duesseldorf.de about your
+$0: system, including any error possibly output before this
$0: message. Then install a modern shell, or manually run
$0: the script under such a shell if you do have one."
fi
@@ -580,9 +580,9 @@ MAKEFLAGS=
# Identity of this package.
PACKAGE_NAME='sybilSBML'
PACKAGE_TARNAME='sybilsbml'
-PACKAGE_VERSION='2.0.8'
-PACKAGE_STRING='sybilSBML 2.0.8'
-PACKAGE_BUGREPORT='geliudie@uni-duesseldorf.de'
+PACKAGE_VERSION='3.0.0'
+PACKAGE_STRING='sybilSBML 3.0.0'
+PACKAGE_BUGREPORT='clausjonathan.fritzemeier@uni-duesseldorf.de'
PACKAGE_URL=''
# Factoring default headers for most tests.
@@ -1230,7 +1230,7 @@ if test "$ac_init_help" = "long"; then
# Omit some internal or obsolete options to make the list less imposing.
# This message is too long to be a string in the A/UX 3.1 sh.
cat <<_ACEOF
-\`configure' configures sybilSBML 2.0.8 to adapt to many kinds of systems.
+\`configure' configures sybilSBML 3.0.0 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1291,7 +1291,7 @@ fi
if test -n "$ac_init_help"; then
case $ac_init_help in
- short | recursive ) echo "Configuration of sybilSBML 2.0.8:";;
+ short | recursive ) echo "Configuration of sybilSBML 3.0.0:";;
esac
cat <<\_ACEOF
@@ -1315,7 +1315,7 @@ Some influential environment variables:
Use these variables to override the choices made by `configure' or to help
it to find libraries and programs with nonstandard names/locations.
-Report bugs to <geliudie@uni-duesseldorf.de>.
+Report bugs to <clausjonathan.fritzemeier@uni-duesseldorf.de>.
_ACEOF
ac_status=$?
fi
@@ -1378,7 +1378,7 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
-sybilSBML configure 2.0.8
+sybilSBML configure 3.0.0
generated by GNU Autoconf 2.69
Copyright (C) 2012 Free Software Foundation, Inc.
@@ -1537,9 +1537,9 @@ $as_echo "$as_me: WARNING: $2: see the Autoconf documentation" >&2;}
$as_echo "$as_me: WARNING: $2: section \"Present But Cannot Be Compiled\"" >&2;}
{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: proceeding with the compiler's result" >&5
$as_echo "$as_me: WARNING: $2: proceeding with the compiler's result" >&2;}
-( $as_echo "## ------------------------------------------ ##
-## Report this to geliudie@uni-duesseldorf.de ##
-## ------------------------------------------ ##"
+( $as_echo "## ----------------------------------------------------------- ##
+## Report this to clausjonathan.fritzemeier@uni-duesseldorf.de ##
+## ----------------------------------------------------------- ##"
) | sed "s/^/$as_me: WARNING: /" >&2
;;
esac
@@ -1676,11 +1676,78 @@ fi
as_fn_set_status $ac_retval
} # ac_fn_c_try_link
+
+# ac_fn_c_check_func LINENO FUNC VAR
+# ----------------------------------
+# Tests whether FUNC exists, setting the cache variable VAR accordingly
+ac_fn_c_check_func ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
+$as_echo_n "checking for $2... " >&6; }
+if eval \${$3+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+/* Define $2 to an innocuous variant, in case <limits.h> declares $2.
+ For example, HP-UX 11i <limits.h> declares gettimeofday. */
+#define $2 innocuous_$2
+
+/* System header to define __stub macros and hopefully few prototypes,
+ which can conflict with char $2 (); below.
+ Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ <limits.h> exists even on freestanding compilers. */
+
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+
+#undef $2
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char $2 ();
+/* The GNU C library defines this for functions which it implements
+ to always fail with ENOSYS. Some functions are actually named
+ something starting with __ and the normal name is an alias. */
+#if defined __stub_$2 || defined __stub___$2
+choke me
+#endif
+
+int
+main ()
+{
+return $2 ();
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ eval "$3=yes"
+else
+ eval "$3=no"
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+fi
+eval ac_res=\$$3
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+ eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
+
+} # ac_fn_c_check_func
cat >config.log <<_ACEOF
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
-It was created by sybilSBML $as_me 2.0.8, which was
+It was created by sybilSBML $as_me 3.0.0, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ $0 $@
@@ -3528,6 +3595,101 @@ else
fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for readSBML in -lsbml" >&5
+$as_echo_n "checking for readSBML in -lsbml... " >&6; }
+if ${ac_cv_lib_sbml_readSBML+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_check_lib_save_LIBS=$LIBS
+LIBS="-lsbml $LIBS"
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char readSBML ();
+int
+main ()
+{
+return readSBML ();
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ ac_cv_lib_sbml_readSBML=yes
+else
+ ac_cv_lib_sbml_readSBML=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_sbml_readSBML" >&5
+$as_echo "$ac_cv_lib_sbml_readSBML" >&6; }
+if test "x$ac_cv_lib_sbml_readSBML" = xyes; then :
+ cat >>confdefs.h <<_ACEOF
+#define HAVE_LIBSBML 1
+_ACEOF
+
+ LIBS="-lsbml $LIBS"
+
+else
+ as_fn_error $? "Could not link to libSBML:
+ use --with-sbml-lib or PKG_LIBS to specify the library path and the libraries to pass to the linker." "$LINENO" 5
+fi
+
+
+ac_fn_c_check_header_compile "$LINENO" "sbml/packages/fbc/common/FbcExtensionTypes.h" "ac_cv_header_sbml_packages_fbc_common_FbcExtensionTypes_h" "#include <sbml/SBMLTypes.h>
+"
+if test "x$ac_cv_header_sbml_packages_fbc_common_FbcExtensionTypes_h" = xyes; then :
+
+else
+ as_fn_error $? "Could not find specific FBC header of libSBML:
+ make sure your libSBML version is >= 5.13." "$LINENO" 5
+fi
+
+
+
+#AC_CHECK_LIB([sbml], [SBMLExtensionRegistry_getRegisteredPackages], ,
+# AC_MSG_ERROR([Could not find specific FBC function of libSBML:
+# make sure your libSBML version is >= 5.13.]))
+
+for ac_func in SBase_getPlugin SBMLExtensionRegistry_getRegisteredPackages GeneProductAssociation_setAssociation FbcReactionPlugin_getLowerFluxBound
+do :
+ as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh`
+ac_fn_c_check_func "$LINENO" "$ac_func" "$as_ac_var"
+if eval test \"x\$"$as_ac_var"\" = x"yes"; then :
+ cat >>confdefs.h <<_ACEOF
+#define `$as_echo "HAVE_$ac_func" | $as_tr_cpp` 1
+_ACEOF
+
+else
+ as_fn_error $? "Could not find specific FBC function of libSBML:
+ make sure your libSBML version is >= 5.13." "$LINENO" 5
+fi
+done
+
+
+#AC_SEARCH_LIBS([SBase_getPlugin], [sbml], ,
+# AC_MSG_ERROR([Could not find specific FBC function of libSBML:
+# make sure your libSBML version is >= 5.13.]))
+
+#AC_SEARCH_LIBS([SBMLExtensionRegistry_getRegisteredPackages], [sbml], ,
+# AC_MSG_ERROR([Could not find specific FBC function of libSBML:
+# make sure your libSBML version is >= 5.13.]))
+
+
+
+#AC_SEARCH_LIBS([GeneProductAssociation_setAssociation], [sbml], ,
+# AC_MSG_ERROR([Could not find specific FBC function of libSBML:
+# make sure your libSBML version is >= 5.13.]))
+
+
@@ -4077,7 +4239,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
# report actual input values of CONFIG_FILES etc. instead of their
# values after options handling.
ac_log="
-This file was extended by sybilSBML $as_me 2.0.8, which was
+This file was extended by sybilSBML $as_me 3.0.0, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
@@ -4124,13 +4286,13 @@ Usage: $0 [OPTION]... [TAG]...
Configuration files:
$config_files
-Report bugs to <geliudie@uni-duesseldorf.de>."
+Report bugs to <clausjonathan.fritzemeier@uni-duesseldorf.de>."
_ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\
-sybilSBML config.status 2.0.8
+sybilSBML config.status 3.0.0
configured by $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\"
diff --git a/configure.ac b/configure.ac
index c75e9c7e0a8012cf7e0f97754609a57bea301223..08faede40197a400f9e86fc8520a65aa90f60143 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1,4 +1,4 @@
-AC_INIT([sybilSBML], [2.0.8], [geliudie@uni-duesseldorf.de])
+AC_INIT([sybilSBML], [3.0.0], [clausjonathan.fritzemeier@uni-duesseldorf.de])
dnl # --------------------------------------------------------------------
dnl # global (environment) variables
@@ -236,6 +236,38 @@ AC_SEARCH_LIBS([readSBML], [sbml], ,
AC_MSG_ERROR([Could not link to libSBML:
use --with-sbml-lib or PKG_LIBS to specify the library path and the libraries to pass to the linker.]))
+AC_CHECK_LIB([sbml], [readSBML], ,
+ AC_MSG_ERROR([Could not link to libSBML:
+ use --with-sbml-lib or PKG_LIBS to specify the library path and the libraries to pass to the linker.]))
+
+AC_CHECK_HEADER([sbml/packages/fbc/common/FbcExtensionTypes.h], ,
+ AC_MSG_ERROR([Could not find specific FBC header of libSBML:
+ make sure your libSBML version is >= 5.13.]),
+ [#include <sbml/SBMLTypes.h>])
+
+#AC_CHECK_LIB([sbml], [SBMLExtensionRegistry_getRegisteredPackages], ,
+# AC_MSG_ERROR([Could not find specific FBC function of libSBML:
+# make sure your libSBML version is >= 5.13.]))
+
+AC_CHECK_FUNCS([SBase_getPlugin SBMLExtensionRegistry_getRegisteredPackages GeneProductAssociation_setAssociation FbcReactionPlugin_getLowerFluxBound], ,
+ AC_MSG_ERROR([Could not find specific FBC function of libSBML:
+ make sure your libSBML version is >= 5.13.]))
+
+#AC_SEARCH_LIBS([SBase_getPlugin], [sbml], ,
+# AC_MSG_ERROR([Could not find specific FBC function of libSBML:
+# make sure your libSBML version is >= 5.13.]))
+
+#AC_SEARCH_LIBS([SBMLExtensionRegistry_getRegisteredPackages], [sbml], ,
+# AC_MSG_ERROR([Could not find specific FBC function of libSBML:
+# make sure your libSBML version is >= 5.13.]))
+
+
+
+#AC_SEARCH_LIBS([GeneProductAssociation_setAssociation], [sbml], ,
+# AC_MSG_ERROR([Could not find specific FBC function of libSBML:
+# make sure your libSBML version is >= 5.13.]))
+
+
dnl # --------------------------------------------------------------------
dnl # substitute src/Makevars